Abstract Graphene oxide/attapulgite (GO/APT) composite membranes were successfully fabricated by the vacuum-assisted filtration for efficient dyes wastewater treatment. By characterization of FTIR, XPS, Raman, XRD and FESEM, APT nanorods were confirmed to be incorporated into GO laminar layers via grafting modification, which would influence GO interlayer distance (d-spacing), membrane surface microstructure (laminate morphology, structure, and hydrophilicity) and even water separation performance. Comparison of those of pristine GO membrane, the calculated d-spacing of GO/APT membranes gradually increased from 0.90 nm to 1.07 nm, while water contact angles decreased from 71.0° to 43.3° with the increasing APT/GO ratios. Moreover, GO/APT membranes exhibited rough hierarchical microstructure and higher surface hydrophilicity, which was in conjunction with larger interlayer spacing to synergistically improve separation performance. The water permeated flux increased from 3.4 of pristine GO membrane to 13.3 L m−2 h−1 of GO/APT membrane with preserving high rejection nearly to 100% for 7.5 mg L−1 Rh B wastewater under optimized conditions. Similarly, membrane thickness, dye concentrations and separating species in feed solutions were also found to affect membrane separation performance. Dye molecules were efficiently rejected through GO/APT nanofiltration membranes by the synergistic separation mechanism: size exclusion effect because of the unimpeded water channels formed into 3D network laminate structure, and electrostatic interactions between the oxygen-containing functional groups on membrane surface and charged molecules. Such these GO/APT membranes demonstrated efficiently separation properties and thus provided new insight into the potential applications in water purification and dyes wastewater treatment.